Then again, maybe they didn't have good reason. Baybe does not establish anything. Define Good Reason by their society and rules.
Truth is, we don't know enough about that conflict.
What we DO know is that the Baku were being forced out of their homes, that they had lived in peacefully, bothering nobody, for hundreds of years.
It was a society, in and of itself. A colony from elsewhere on inception? Irrelevant morally, if interesting.
Until the Son'a and Federation situations, it was very productive to live there without depending on their technological knowledge.
Being where they are, and hard to reach, unnoticed, made more sense given their origins.